diff tools/protein_analysis/wolf_psort.py @ 20:a19b3ded8f33 draft

v0.2.11 Job splitting fast-fail; RXLR tools supports HMMER2 from BioConda; Capture more version information; misc internal changes

--- a/tools/protein_analysis/wolf_psort.py	Wed Feb 01 09:46:42 2017 -0500
+++ b/tools/protein_analysis/wolf_psort.py	Thu Sep 21 11:35:20 2017 -0400
@@ -33,9 +33,13 @@
 normally use Python's multiprocessing library in this situation but it requires
 at least Python 2.6 and at the time of writing Galaxy still supports Python 2.4.
 """
-import sys
+
+from __future__ import print_function
+
 import os
-from seq_analysis_utils import split_fasta, run_jobs, thread_count
+import sys
+
+from seq_analysis_utils import run_jobs, split_fasta, thread_count
 
 FASTA_CHUNK = 500
 exe = "runWolfPsortSummary"
@@ -61,6 +65,9 @@
 https://lists.galaxyproject.org/pipermail/galaxy-dev/2015-December/023386.html
 """
 
+if "-v" in sys.argv or "--version" in sys.argv:
+    sys.exit("WoLF-PSORT wrapper version 0.0.11")
+
 if len(sys.argv) != 5:
     sys.exit("Require four arguments, organism, threads, input protein FASTA file & output tabular file")
 
@@ -84,6 +91,7 @@
             out_handle.write("%s\t%s\t%s\t%i\n"
                              % (name, comp, score, rank + 1))
 
+
 fasta_files = split_fasta(fasta_file, tabular_file, n=FASTA_CHUNK)
 temp_files = [f + ".out" for f in fasta_files]
 assert len(fasta_files) == len(temp_files)
@@ -97,9 +105,10 @@
         if os.path.isfile(f):
             os.remove(f)
 
+
 if len(jobs) > 1 and num_threads > 1:
     # A small "info" message for Galaxy to show the user.
-    print "Using %i threads for %i tasks" % (min(num_threads, len(jobs)), len(jobs))
+    print("Using %i threads for %i tasks" % (min(num_threads, len(jobs)), len(jobs)))
 results = run_jobs(jobs, num_threads)
 assert len(fasta_files) == len(temp_files) == len(jobs)
 for fasta, temp, cmd in zip(fasta_files, temp_files, jobs):